Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011587.1 Corchorus capsularis cultivar CVL-1 contig11608, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35517
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3395 original size:16 final size:16
Alignment explanation
Indices: 3350--3422 Score: 67
Period size: 17 Copynumber: 4.5 Consensus size: 16
3340 TCAGGCTGTT
*
3350 TTCGGGTCGGGTTTAA
1 TTCGGGTCGGGTTAAA
* * *
3366 GTCGGATTCCGGTTAAA
1 TTCGG-GTCGGGTTAAA
*
3383 TTTGGGTCGGGTT-AA
1 TTCGGGTCGGGTTAAA
*
3398 TTCGGGTTCGGATTAAA
1 TTCGGG-TCGGGTTAAA
3415 TTCGGGTC
1 TTCGGGTC
3423 AGATTGATTC
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
15 7 0.16
16 18 0.41
17 19 0.43
ACGTcount: A:0.16, C:0.14, G:0.34, T:0.36
Consensus pattern (16 bp):
TTCGGGTCGGGTTAAA
Found at i:3422 original size:32 final size:31
Alignment explanation
Indices: 3350--3471 Score: 100
Period size: 32 Copynumber: 3.8 Consensus size: 31
3340 TCAGGCTGTT
*
3350 TTCGGGTCGGGTTTAAGTCGGATTCCGGTTAAA
1 TTCGGGTCGGG-TTAATTCGGATT-CGGTTAAA
* *
3383 TTTGGGTCGGGTTAATTCGGGTTCGGATTAAA
1 TTCGGGTCGGGTTAATTCGGATTCGG-TTAAA
* * * * ** *
3415 TTCGGGTCAGATTGATTCGGCTTCGGGCCAAT
1 TTCGGGTCGGGTTAATTCGGATTC-GGTTAAA
* *
3447 TTAGGGTCAGGTTAATTCGGATTCG
1 TTCGGGTCGGGTTAATTCGGATTCG
3472 CGTTCGGATT
Statistics
Matches: 72, Mismatches: 15, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
31 4 0.06
32 56 0.78
33 12 0.17
ACGTcount: A:0.18, C:0.15, G:0.33, T:0.34
Consensus pattern (31 bp):
TTCGGGTCGGGTTAATTCGGATTCGGTTAAA
Found at i:3427 original size:16 final size:16
Alignment explanation
Indices: 3378--3427 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
3368 CGGATTCCGG
* *
3378 TTAAATTTGGGTCGGG
1 TTAAATTCGGGTCGGA
3394 TT-AATTCGGGTTCGGA
1 TTAAATTCGGG-TCGGA
*
3410 TTAAATTCGGGTCAGA
1 TTAAATTCGGGTCGGA
3426 TT
1 TT
3428 GATTCGGCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 7 0.24
16 14 0.48
17 8 0.28
ACGTcount: A:0.22, C:0.10, G:0.30, T:0.38
Consensus pattern (16 bp):
TTAAATTCGGGTCGGA
Found at i:3713 original size:17 final size:17
Alignment explanation
Indices: 3671--3710 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
3661 GTTTTTCAGG
3671 TTCGGGTTC-GGTTTTT
1 TTCGGGTTCAGGTTTTT
*
3687 TTCGAGTTCAGG-TTTT
1 TTCGGGTTCAGGTTTTT
3703 TTCGGGTT
1 TTCGGGTT
3711 TCAAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 19 0.90
17 2 0.10
ACGTcount: A:0.05, C:0.12, G:0.30, T:0.53
Consensus pattern (17 bp):
TTCGGGTTCAGGTTTTT
Found at i:4020 original size:2 final size:2
Alignment explanation
Indices: 4007--4039 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3997 CATGTGTACT
*
4007 TA TA TG TA TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4040 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4026 original size:15 final size:15
Alignment explanation
Indices: 4006--4036 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3996 CCATGTGTAC
*
4006 TTATATGTATATATA
1 TTATATATATATATA
4021 TTATATATATATATA
1 TTATATATATATATA
4036 T
1 T
4037 ATAGAGAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATATATATATATA
Found at i:6093 original size:16 final size:16
Alignment explanation
Indices: 6072--6116 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
6062 ATAGTATAGC
*
6072 TTTTTTTTGGCTACAT
1 TTTTTTTTGGCTACAA
*
6088 TTTTTTTTGGTTA-AA
1 TTTTTTTTGGCTACAA
6103 TTTTTTTTGGCTAC
1 TTTTTTTTGGCTAC
6117 TTGAAAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.13, C:0.09, G:0.13, T:0.64
Consensus pattern (16 bp):
TTTTTTTTGGCTACAA
Found at i:18183 original size:60 final size:60
Alignment explanation
Indices: 18110--18272 Score: 213
Period size: 60 Copynumber: 2.7 Consensus size: 60
18100 TTTTGGCTAA
* * * * *
18110 TTGGTCAAATAAGGGCTTAACA-TTTTCTAAAATGTTCAAATAAGAGCCCGATCTTTTAAT
1 TTGGCCAAATAAGGGCATAA-AGTTATCGAAAATGCTCAAATAAGAGCCCGATCTTTTAAT
* *
18170 TTGGCCAAATAAGGGCATAAAGTTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAAT
1 TTGGCCAAATAAGGGCATAAAGTTATCGAAAATGCTCAAATAAGAGCCCGATCTTTTAAT
* * *
18230 TTGACCAAATAAGGGCCTAATG-TATCGAAAATGCTCAAATAAG
1 TTGGCCAAATAAGGGCATAAAGTTATCGAAAATGCTCAAATAAG
18273 GGCATGGCGT
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
59 22 0.24
60 70 0.76
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (60 bp):
TTGGCCAAATAAGGGCATAAAGTTATCGAAAATGCTCAAATAAGAGCCCGATCTTTTAAT
Found at i:18271 original size:30 final size:30
Alignment explanation
Indices: 18175--18275 Score: 82
Period size: 29 Copynumber: 3.4 Consensus size: 30
18165 TTAATTTGGC
* *
18175 CAAATAAGGGCATAAAGTTATCGAAAATGCT
1 CAAATAAGGGCCTAATG-TATCGAAAATGCT
* * ** **
18206 CAAATAAGGGTCC-GATCT-TTTAATTTGAC-
1 CAAATAAGGG-CCTAATGTATCGAAAATG-CT
18235 CAAATAAGGGCCTAATGTATCGAAAATGCT
1 CAAATAAGGGCCTAATGTATCGAAAATGCT
18265 CAAATAAGGGC
1 CAAATAAGGGC
18276 ATGGCGTCAG
Statistics
Matches: 51, Mismatches: 14, Indels: 11
0.67 0.18 0.14
Matches are distributed among these distances:
28 2 0.04
29 19 0.37
30 18 0.35
31 11 0.22
32 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.25
Consensus pattern (30 bp):
CAAATAAGGGCCTAATGTATCGAAAATGCT
Found at i:24867 original size:49 final size:49
Alignment explanation
Indices: 24825--25503 Score: 742
Period size: 49 Copynumber: 13.9 Consensus size: 49
24815 TTACTTACAT
*
24825 TTTCCCAAAACGCCCTTCCCAAACGGAAGCCATTCATTTTTACTTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA
* * * * *
24874 TTTCCCAAACCACCCTTCCCAGACGAAAGCCATTAATCTTTACTTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA
* *
24923 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATCTTTACGTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA
* * * *
24972 TCTCCCAAAACACCCTTCCTAGACGGAAGCCACTT-A-TTTTACTTGCTT
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCA-TTCATTTTTACTTGCTA
* * *
25020 TTTTCTAAAACACCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA
* * * *
25069 TTTCCCAAAGCGCCCTTCCCAAACGGAAGCCATTTATCTTTACTTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA
* * *
25118 TTTCCCAAAACGCCCTTCCCAGACGGAAGTCATTCATCTTTACGTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA
* * * * *
25167 TCTCCCAAAACACCCTTCCCAGACGAAAGCCATTTATTTTTACTTGTTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA
* * * *
25216 TTTCCCAAAGCGGCCTTCCCAGACGGAAGCCACTT-TTTTTTACCTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCA-TTCATTTTTACTTGCTA
* * * * *
25265 TTTCCCAAAATGCCCTTCCCGGACGGAAGCCACTCTTTTTTACCTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA
* * * ** * *
25314 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACCCTTTTTTACCTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA
* * * * *
25363 TTTCCCAAGATGCCCTTCCTAGACGGAAGGCACTT-A-TTTTACTTGCTT
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCA-TTCATTTTTACTTGCTA
* * * * *
25411 TTTCCCAAAAACGCCCTTCCCGGACAGAAGGCACTT-TTTTTTACCTGCT-
1 TTTCCC-AAAACGCCCTTCCCAGACGGAAGCCA-TTCATTTTTACTTGCTA
* * * * *
25460 TTCCCCAAAACGCCCTTCCCGGACGGAAGGCGTTAATTTTTACT
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACT
25504 CACTTTTTTC
Statistics
Matches: 544, Mismatches: 77, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
47 4 0.01
48 86 0.16
49 440 0.81
50 14 0.03
ACGTcount: A:0.24, C:0.32, G:0.13, T:0.30
Consensus pattern (49 bp):
TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA
Found at i:29426 original size:15 final size:14
Alignment explanation
Indices: 29406--29457 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
29396 CAAGAGACGT
29406 TTTTCAAAAAAATGG
1 TTTTCAAAAAAA-GG
*
29421 TTTTCAAGAAAAGG
1 TTTTCAAAAAAAGG
*
29435 TTTTCGAAAATAA-G
1 TTTTC-AAAAAAAGG
*
29449 TTTACAAAA
1 TTTTCAAAA
29458 GGTTTTTAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 4 0.12
14 12 0.38
15 16 0.50
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (14 bp):
TTTTCAAAAAAAGG
Found at i:29438 original size:14 final size:15
Alignment explanation
Indices: 29406--29444 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
29396 CAAGAGACGT
29406 TTTTCAAAAAAATGG
1 TTTTCAAAAAAATGG
*
29421 TTTTCAAGAAAA-GG
1 TTTTCAAAAAAATGG
29435 TTTTCGAAAA
1 TTTTC-AAAA
29445 TAAGTTTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (15 bp):
TTTTCAAAAAAATGG
Found at i:30211 original size:94 final size:96
Alignment explanation
Indices: 30043--30216 Score: 282
Period size: 94 Copynumber: 1.8 Consensus size: 96
30033 CAAATTTGTC
* * *
30043 TTTGCAAAAGAAAAGTGTTTTTTCTCGAAAAAGGTTTTTAGCGAAAAGTGGTTTCAAAAGTTTTT
1 TTTGCAAAAGAAAAGTGTGTTTTCTCGAAAAAGGTTTTTAGAGAAAACTGGTTTCAAAAGTTTTT
30108 CAAAGGCAAGCGCATAGTACAAGAAATAGGT
66 CAAAGGCAAGCGCATAGTACAAGAAATAGGT
*
30139 TTTGCAAAAGAAACGTGTGTTTTCTC-AAAAAGG-TTTTAGAGAAAACTGGTTTCAAAAGTTTTT
1 TTTGCAAAAGAAAAGTGTGTTTTCTCGAAAAAGGTTTTTAGAGAAAACTGGTTTCAAAAGTTTTT
30202 CGAAA-GCAAGCGCAT
66 C-AAAGGCAAGCGCAT
30217 GAAAAAGAGA
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
94 39 0.53
95 10 0.14
96 24 0.33
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.30
Consensus pattern (96 bp):
TTTGCAAAAGAAAAGTGTGTTTTCTCGAAAAAGGTTTTTAGAGAAAACTGGTTTCAAAAGTTTTT
CAAAGGCAAGCGCATAGTACAAGAAATAGGT
Found at i:31426 original size:74 final size:73
Alignment explanation
Indices: 31329--31584 Score: 243
Period size: 77 Copynumber: 3.4 Consensus size: 73
31319 AAATTATCAA
* * * * *
31329 AGTT-GACTGGAAACAGGTTATCTTTCAGCAATTATCTTACGACTGGAAACAGATCGTCTTTCAG
1 AGTTCGACTGGAAACAGGTCATCTTTCAACAATTATCTTATGACTGGAAACAGGTCATCTTTCAG
*
31393 CACTTATT
66 CAATTATT
* **
31401 AGGTTCGACTGGAAACAGGTCATCTTTCAATAAGTTATCAAAGTTGACTGGAAACAGGTCATCTT
1 A-GTTCGACTGGAAACAGGTCATCTTTCAACAA-TTATCTTA--TGACTGGAAACAGGTCATCTT
31466 TCAGCAATTATCT
62 TCAGCAATTAT-T
* * * *
31479 --TACGACTGGAAACAGGTCGTCTTTCAACACTTGTTCAGTT-TGACTGGAAACAGGTCATCTTT
1 AGTTCGACTGGAAACAGGTCATCTTTCAACAATT-ATC--TTATGACTGGAAACAGGTCATCTTT
*
31541 C-GACAAGTTATCA
63 CAG-CAA-TTAT-T
*
31554 AGATCGACTGGAAACAGGTCATCTTTCAACA
1 AGTTCGACTGGAAACAGGTCATCTTTCAACA
31585 GTTTTCAGTT
Statistics
Matches: 151, Mismatches: 20, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
72 1 0.01
73 4 0.03
74 52 0.34
75 39 0.26
77 54 0.36
78 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (73 bp):
AGTTCGACTGGAAACAGGTCATCTTTCAACAATTATCTTATGACTGGAAACAGGTCATCTTTCAG
CAATTATT
Found at i:31456 original size:39 final size:38
Alignment explanation
Indices: 31320--31584 Score: 247
Period size: 38 Copynumber: 7.0 Consensus size: 38
31310 TCATCTTCCA
* * *
31320 AATTATCAAAGTTGACTGGAAACAGGTTATCTTTCAGC
1 AATTATCTAAGTTGACTGGAAACAGGTCATCTTTCAAC
* * * * *
31358 AATTATCTTA--CGACTGGAAACAGATCGTCTTTCAGC
1 AATTATCTAAGTTGACTGGAAACAGGTCATCTTTCAAC
* * *
31394 ACTTAT-TAGGTTCGACTGGAAACAGGTCATCTTTCAAT
1 AATTATCTAAGTT-GACTGGAAACAGGTCATCTTTCAAC
* *
31432 AAGTTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGC
1 AA-TTATCTAAGTTGACTGGAAACAGGTCATCTTTCAAC
* * *
31471 AATTATCTTA--CGACTGGAAACAGGTCGTCTTTCAAC
1 AATTATCTAAGTTGACTGGAAACAGGTCATCTTTCAAC
* * * *
31507 ACTTGT-TCAGTTTGACTGGAAACAGGTCATCTTTCGAC
1 AATTATCTAAG-TTGACTGGAAACAGGTCATCTTTCAAC
*
31545 AAGTTATC-AAGATCGACTGGAAACAGGTCATCTTTCAAC
1 AA-TTATCTAAG-TTGACTGGAAACAGGTCATCTTTCAAC
31584 A
1 A
31585 GTTTTCAGTT
Statistics
Matches: 181, Mismatches: 36, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
35 3 0.02
36 54 0.30
38 60 0.33
39 60 0.33
40 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (38 bp):
AATTATCTAAGTTGACTGGAAACAGGTCATCTTTCAAC
Found at i:31471 original size:77 final size:75
Alignment explanation
Indices: 31329--31582 Score: 231
Period size: 74 Copynumber: 3.4 Consensus size: 75
31319 AAATTATCAA
* * * * *
31329 AGTT-GACTGGAAACAGGTTATCTTTCAGCAA-TT-ATC--TTACGACTGGAAACAGATCGTCTT
1 AGTTCGACTGGAAACAGGTCATCTTTCA-AAACTTGATCAGTT-TGACTGGAAACAGGTCATCTT
*
31389 TCAGCACTTATT
64 TCAGCAATTATT
*
31401 AGGTTCGACTGGAAACAGGTCATCTTTCAATAAGTT-ATCAAAG-TTGACTGGAAACAGGTCATC
1 A-GTTCGACTGGAAACAGGTCATCTTTCAA-AACTTGATC--AGTTTGACTGGAAACAGGTCATC
31464 TTTCAGCAATTATCT
62 TTTCAGCAATTAT-T
* * * *
31479 --TACGACTGGAAACAGGTCGTCTTTCAACACTTGTTCAGTTTGACTGGAAACAGGTCATCTTTC
1 AGTTCGACTGGAAACAGGTCATCTTTCAAAACTTGATCAGTTTGACTGGAAACAGGTCATCTTTC
*
31542 -GACAAGTTATCA
66 AG-CAA-TTAT-T
*
31554 AGATCGACTGGAAACAGGTCATCTTTCAA
1 AGTTCGACTGGAAACAGGTCATCTTTCAA
31583 CAGTTTTCAG
Statistics
Matches: 152, Mismatches: 15, Indels: 25
0.79 0.08 0.13
Matches are distributed among these distances:
72 1 0.01
73 6 0.04
74 54 0.36
75 37 0.24
77 52 0.34
78 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (75 bp):
AGTTCGACTGGAAACAGGTCATCTTTCAAAACTTGATCAGTTTGACTGGAAACAGGTCATCTTTC
AGCAATTATT
Found at i:31524 original size:113 final size:113
Alignment explanation
Indices: 31322--31581 Score: 416
Period size: 113 Copynumber: 2.3 Consensus size: 113
31312 ATCTTCCAAA
*
31322 TTATCAAAGTTGACTGGAAACAGGTTATCTTTCAGCAATTATCTTACGACTGGAAACAGATCGTC
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGACTGGAAACAGATCGTC
* *
31387 TTTCAGCACTTATTAGGTTCGACTGGAAACAGGTCATCTTTCAATAAG
66 TTTCAACACTTATTAGGTTCGACTGGAAACAGGTCATCTTTCAACAAG
*
31435 TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGACTGGAAACAGGTCGTC
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGACTGGAAACAGATCGTC
* * *
31500 TTTCAACACTTGTTCA-GTTTGACTGGAAACAGGTCATCTTTCGACAAG
66 TTTCAACACTTATT-AGGTTCGACTGGAAACAGGTCATCTTTCAACAAG
*
31548 TTATC-AAGATCGACTGGAAACAGGTCATCTTTCA
1 TTATCAAAG-TTGACTGGAAACAGGTCATCTTTCA
31582 ACAGTTTTCA
Statistics
Matches: 137, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
112 3 0.02
113 133 0.97
114 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (113 bp):
TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGACTGGAAACAGATCGTC
TTTCAACACTTATTAGGTTCGACTGGAAACAGGTCATCTTTCAACAAG
Found at i:31658 original size:34 final size:34
Alignment explanation
Indices: 31619--31699 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
31609 CATTTCAACA
* *
31619 AATTTTCAACTTTACAGCATTTC-AACAACTTCTC
1 AATTTTCAACTTTACAGCACTCCGAA-AACTTCTC
* *
31653 AATTTTCAACTTTACCGCACTCCGAAAACTTTTC
1 AATTTTCAACTTTACAGCACTCCGAAAACTTCTC
*
31687 AATTTACAACTTT
1 AATTTTCAACTTT
31700 TCAGTTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
34 39 0.95
35 2 0.05
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (34 bp):
AATTTTCAACTTTACAGCACTCCGAAAACTTCTC
Found at i:31699 original size:15 final size:15
Alignment explanation
Indices: 31679--31762 Score: 114
Period size: 15 Copynumber: 5.3 Consensus size: 15
31669 GCACTCCGAA
31679 AACTTTTCAATTTAC
1 AACTTTTCAATTTAC
*
31694 AACTTTTCAGTTTTTAC
1 AACTTTTCA--ATTTAC
31711 AACTTTTTCAATTTAC
1 AAC-TTTTCAATTTAC
31727 AACTTTTTCAATTTAC
1 AAC-TTTTCAATTTAC
*
31743 AACTTTTCAATTGAC
1 AACTTTTCAATTTAC
31758 AACTT
1 AACTT
31763 CCATATGAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
15 25 0.40
16 24 0.38
17 8 0.13
18 6 0.10
ACGTcount: A:0.31, C:0.19, G:0.02, T:0.48
Consensus pattern (15 bp):
AACTTTTCAATTTAC
Found at i:31727 original size:16 final size:16
Alignment explanation
Indices: 31682--31762 Score: 112
Period size: 16 Copynumber: 5.1 Consensus size: 16
31672 CTCCGAAAAC
31682 TTTTCAATTTACAAC-
1 TTTTCAATTTACAACT
*
31697 TTTTCAGTTTTTACAACT
1 TTTTCA--ATTTACAACT
31715 TTTTCAATTTACAACT
1 TTTTCAATTTACAACT
31731 TTTTCAATTTACAAC-
1 TTTTCAATTTACAACT
*
31746 TTTTCAATTGACAACT
1 TTTTCAATTTACAACT
31762 T
1 T
31763 CCATATGAGT
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
15 20 0.34
16 25 0.42
17 8 0.14
18 6 0.10
ACGTcount: A:0.30, C:0.19, G:0.02, T:0.49
Consensus pattern (16 bp):
TTTTCAATTTACAACT
Found at i:31839 original size:48 final size:47
Alignment explanation
Indices: 31759--31905 Score: 213
Period size: 47 Copynumber: 3.1 Consensus size: 47
31749 TCAATTGACA
* *
31759 ACTTCCATATGAGTCAGCAATCATTCGACCCAAGTTGGTCTTTCCTC
1 ACTTCCATGTGAGTCAGAAATCATTCGACCCAAGTTGGTCTTTCCTC
* *
31806 ACTTCCATGTGAATCAGAAATCGTTCCGACCCAAGTTGGTCTTTCCTC
1 ACTTCCATGTGAGTCAGAAATCATT-CGACCCAAGTTGGTCTTTCCTC
* * * *
31854 ACTTCCATGTGAGTCAGAAGTCCTTCGACCAAAGTTGGTCTTTTCTC
1 ACTTCCATGTGAGTCAGAAATCATTCGACCCAAGTTGGTCTTTCCTC
31901 ACTTC
1 ACTTC
31906 TATGAAAAGT
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
47 46 0.51
48 44 0.49
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (47 bp):
ACTTCCATGTGAGTCAGAAATCATTCGACCCAAGTTGGTCTTTCCTC
Found at i:34409 original size:89 final size:82
Alignment explanation
Indices: 34267--34433 Score: 253
Period size: 82 Copynumber: 2.0 Consensus size: 82
34257 GAGAAAATTC
34267 AAAAGGAGGGTGGATAGTTTTGGTTCTTCAGGGTAGTAAAAAAAAAATAGGGAGAAGTAAGTAGA
1 AAAAGGAGGGTGGATAGTTTTGGTTCTTCAGGGTAGTAAAAAAAAAATAGGGAGAAGTAAGTAGA
*
34332 GTTTCATTTTTTTAAAG
66 GATTCATTTTTTTAAAG
34349 AAAAGGAGGGTGGATAGTTTTGGTTCTTCAGGGTAGTAAAAAAATAAAATAAAATAGGGAGAAGT
1 AAAAGGAGGGTGGATAGTTTTGGTTCTTCAGGGTAGT-----AA-AAAA-AAAATAGGGAGAAGT
*
34414 CAGTAGAGATTCATTTTTTT
59 AAGTAGAGATTCATTTTTTT
34434 TTTTAAAAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 7
0.89 0.02 0.08
Matches are distributed among these distances:
82 37 0.49
87 2 0.03
88 4 0.05
89 33 0.43
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (82 bp):
AAAAGGAGGGTGGATAGTTTTGGTTCTTCAGGGTAGTAAAAAAAAAATAGGGAGAAGTAAGTAGA
GATTCATTTTTTTAAAG
Found at i:34489 original size:25 final size:27
Alignment explanation
Indices: 34443--34500 Score: 84
Period size: 25 Copynumber: 2.2 Consensus size: 27
34433 TTTTTAAAAA
*
34443 AAGGATCGGTTTGAGAACAAAAAAAGG
1 AAGGGTCGGTTTGAGAACAAAAAAAGG
*
34470 AAGGGTCGGTTTTA-AA-AAAAAAAGG
1 AAGGGTCGGTTTGAGAACAAAAAAAGG
34495 AAGGGT
1 AAGGGT
34501 AGGTAGATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 15 0.52
26 2 0.07
27 12 0.41
ACGTcount: A:0.47, C:0.05, G:0.31, T:0.17
Consensus pattern (27 bp):
AAGGGTCGGTTTGAGAACAAAAAAAGG
Done.